Hi Kevin,
Can you explain the problem a bit more detailed?
You mentioned that when you press "Ref all home" button Mach thinks that your axis is already at home, right?
From what do you think that Mach is thinking this way?
What happens when you press the Ref all home button, axis starts to move, or not moves at all?
Any text appears in the "Status" field? (right next to e-stop button)
I think you should write down step by step what you do and what happens to let me see things closer.
Also a wiring diagram of your limit/home switches may help some.
Did you try to home axis separately? Go to diagnostics screen and there is RefX, RefY, RefZ etc. buttons,
so you can test axis homing separately, hopefully then you can locate the error if it is a connection problem or noise on an input.
And as Ian and Hood mentioned you cannot disable the external E-stop, ofcourse there is a trick to disable it with writing a port number which not exist, e.g. port 0 into e-stop setup, but this is not recommended, because it will leaves the machine without safety, so don't do this....
Cheers,
Balazs